1
|
Zhang S, Xu R, Hu M, Choueiry F, Jin N, Li J, Mo X, Zhu J. Distinct plasma molecular profiles between early-onset and late-onset colorectal cancer patients revealed by metabolic and lipidomic analyses. J Pharm Biomed Anal 2024; 241:115978. [PMID: 38237540 DOI: 10.1016/j.jpba.2024.115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
Colorectal cancer (CRC) incidence in younger adults has been steadily rising, warranting an in-depth investigation into the distinctions between early-onset CRC (EOCRC, < 50 years) and late-onset CRC (LOCRC, ≥ 50 years). Despite extensive study of clinical, pathological, and molecular traits, differentiating EOCRC from LOCRC and identifying potential biomarkers remain elusive. We analyzed plasma samples from healthy individuals, EOCRC, and LOCRC patients using liquid-chromatography mass spectrometry (LC/MS)-based metabolomics and lipidomics. Distinct polar metabolite and lipid profiles with significant metabolites altered in CRC group (e.g., choline and DG 40:4) were identified. Notably, EOCRC exhibited distinct polar metabolomic and differential lipidomic profiles compared to LOCRC, with polar metabolites like aminoadipate and uridine contributing significantly to the difference, and originating from pathways such as lysine biosynthesis and nucleotide metabolism. Furthermore, gene set enrichment analysis (GSEA) using independent TCGA gene expression data identified pathways significantly enriched in either EOCRC or LOCRC. Integrating gene expression and metabolomics data revealed numerous associations differentiating EOCRC and LOCRC. Our multi-omics integration underscores critical molecular distinctions, offers insights into the EOCRC development mechanisms and potential plasma biomarkers for diagnosis.
Collapse
Affiliation(s)
- Shiqi Zhang
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Rui Xu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Ming Hu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Fouad Choueiry
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Ning Jin
- Medical Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Jieli Li
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaokui Mo
- Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Jiangjiang Zhu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
2
|
Acar C, Celik SK, Ozdemirel HO, Tuncdemir BE, Alan S, Mergen H. Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer. Folia Microbiol (Praha) 2024; 69:333-345. [PMID: 37344611 DOI: 10.1007/s12223-023-01072-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.
Collapse
Affiliation(s)
- Ceren Acar
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Inonu University, Malatya, 44280, Turkey.
| | | | - H Ozgur Ozdemirel
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Beril Erdem Tuncdemir
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Saadet Alan
- Faculty of Medicine, Department of Medical Pathology, Inonu University, Malatya, 44000, Turkey
| | - Hatice Mergen
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| |
Collapse
|
3
|
Órdenes P, Carril Pardo C, Elizondo-Vega R, Oyarce K. Current Research on Molecular Biomarkers for Colorectal Cancer in Stool Samples. Biology (Basel) 2023; 13:15. [PMID: 38248446 PMCID: PMC10813333 DOI: 10.3390/biology13010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/23/2024]
Abstract
Colorectal cancer (CRC) is one of the most diagnosed cancers worldwide, with a high incidence and mortality rate when diagnosed late. Currently, the methods used in healthcare to diagnose CRC are the fecal occult blood test, flexible sigmoidoscopy, and colonoscopy. However, the lack of sensitivity and specificity and low population adherence are driving the need to implement other technologies that can identify biomarkers that not only help with early CRC detection but allow for the selection of more personalized treatment options. In this regard, the implementation of omics technologies, which can screen large pools of biological molecules, coupled with molecular validation, stands out as a promising tool for the discovery of new biomarkers from biopsied tissues or body fluids. This review delves into the current state of the art in the identification of novel CRC biomarkers that can distinguish cancerous tissue, specifically from fecal samples, as this could be the least invasive approach.
Collapse
Affiliation(s)
- Patricio Órdenes
- Laboratorio de Neuroinmunología, Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede Concepción, Concepción 4030000, Chile; (P.Ó.); (C.C.P.)
| | - Claudio Carril Pardo
- Laboratorio de Neuroinmunología, Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede Concepción, Concepción 4030000, Chile; (P.Ó.); (C.C.P.)
| | - Roberto Elizondo-Vega
- Laboratorio de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070386, Chile;
| | - Karina Oyarce
- Laboratorio de Neuroinmunología, Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede Concepción, Concepción 4030000, Chile; (P.Ó.); (C.C.P.)
| |
Collapse
|
4
|
Aparicio A, Sun Z, Gold DR, Litonjua AA, Weiss ST, Lee-Sarwar K, Liu YY. Genotype-microbiome-metabolome associations in early childhood, and their link to BMI and childhood obesity. medRxiv 2023:2023.11.13.23298467. [PMID: 38014043 PMCID: PMC10680902 DOI: 10.1101/2023.11.13.23298467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The influence of genotype on defining the human gut microbiome has been extensively studied, but definite conclusions have not yet been found. To fill this knowledge gap, we leverage data from children enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART) from 6 months to 8 years old. We focus on a pool of 12 genes previously found to be associated with the gut microbiome in independent studies, establishing a Bonferroni corrected significance level of p-value < 2.29 × 10 -6 . We identified significant associations between SNPs in the FHIT gene (known to be associated with obesity and type 2 diabetes) and obesity-related microbiome features, and the children's BMI through their childhood. Based on these associations, we defined a set of SNPs of interest and a set of taxa of interest. Taking a multi-omics approach, we integrated plasma metabolome data into our analysis and found simultaneous associations among children's BMI, the SNPs of interest, and the taxa of interest, involving amino acids, lipids, nucleotides, and xenobiotics. Using our association results, we constructed a quadripartite graph where each disjoint node set represents SNPs in the FHIT gene, microbial taxa, plasma metabolites, or BMI measurements. Network analysis led to the discovery of patterns that identify several genetic variants, microbial taxa and metabolites as new potential markers for obesity, type 2 diabetes, or insulin resistance risk.
Collapse
|
5
|
Sun L, Qu J, Ke X, Zhang Y, Xu H, Lv N, Leng J, Zhang Y, Guan A, Feng Y, Sun Y. Interaction between intratumoral microbiota and tumor mediates the response of neoadjuvant therapy for rectal cancer. Front Microbiol 2023; 14:1229888. [PMID: 37901832 PMCID: PMC10602640 DOI: 10.3389/fmicb.2023.1229888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Background Previous observations have demonstrated that the response to neoadjuvant chemoradiotherapy (nCRT) is highly variable in patients with locally advanced rectal cancer (LARC). Recent studies focusing on the intratumoral microbiota of colorectal cancer have revealed its role in oncogenesis and tumor progression. However, limited research has focused on the influence of intratumoral microbiota on the nCRT of LARC. Methods We explored the microbial profiles in the tumor microenvironment of LARC using RNA-seq data from a published European cohort. Microbial signatures were characterized in pathological complete response (pCR) and non-pCR groups. Multi-omics analysis was performed between intratumor microbiomes and transcriptomes. Results Microbial α and β diversity were significantly different in pCR and non-pCR groups. Twelve differential microbes were discovered between the pCR and non-pCR groups, six of which were related to subclusters of cancer-associated fibroblasts (CAFs) associated with extracellular matrix formation. A microbial risk score based on the relative abundance of seven differential microbes had predictive value for the nCRT response (AUC = 0.820, p < 0.001). Conclusion Our study presents intratumoral microbes as potential independent predictive markers for the response of nCRT to LARC and demonstrates the underlying mechanism by which the interaction between intratumoral microbes and CAFs mediates the response to nCRT.
Collapse
Affiliation(s)
- Lejia Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Jiangming Qu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xindi Ke
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Hengyi Xu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ning Lv
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingze Leng
- School of Medicine, Tsinghua University, Beijing, China
| | - Yanbin Zhang
- Department of Spine Surgery, Beijing Jishuitan Hospital, Beijing, China
| | - Ai Guan
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yifei Feng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
- Colorectal Institute of Nanjing Medical University, Nanjing, China
| |
Collapse
|
6
|
Qi P, Lv J, Bai LH, Yan XD, Zhang L. Effects of Hypoxemia by Acute High-Altitude Exposure on Human Intestinal Flora and Metabolism. Microorganisms 2023; 11:2284. [PMID: 37764130 PMCID: PMC10535934 DOI: 10.3390/microorganisms11092284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
This study examined the effects of hypoxemia caused by acute high-altitude hypoxia (AHAH) exposure on the human intestinal flora and its metabolites. The changes in the intestinal flora, metabolism, and erythropoietin content in the AHAH population under altitude hypoxia conditions were comprehensively analyzed using 16S rRNA sequencing, metabonomics, and erythropoietin content. The results showed that compared with those in the control group (C group), the flora and metabolites in the hypoxemia group (D group) were altered. We found alterations in the flora according to the metabolic marker tyrosine through random forest and ROC analyses. Fecal and serum metabonomics analyses revealed that microbial metabolites could be absorbed into the blood and participate in human metabolism. Finally, a significant correlation between tyrosine and erythropoietin (EPO) content was found, which shows that human intestinal flora and its metabolites can help to confront altitude stress by regulating EPO levels. Our findings provide new insights into the adaptive mechanism and prevention of AHAH.
Collapse
Affiliation(s)
- Ping Qi
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (P.Q.); (J.L.); (L.-H.B.); (X.-D.Y.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Jin Lv
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (P.Q.); (J.L.); (L.-H.B.); (X.-D.Y.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Liu-Hui Bai
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (P.Q.); (J.L.); (L.-H.B.); (X.-D.Y.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Xiang-Dong Yan
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (P.Q.); (J.L.); (L.-H.B.); (X.-D.Y.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Lei Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (P.Q.); (J.L.); (L.-H.B.); (X.-D.Y.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
7
|
Clavenna MG, La Vecchia M, Sculco M, Joseph S, Barberis E, Amede E, Mellai M, Brossa S, Borgonovi G, Occhipinti P, Boldorini R, Robotti E, Azzimonti B, Bona E, Pasolli E, Ferrante D, Manfredi M, Aspesi A, Dianzani I. Distinct Signatures of Tumor-Associated Microbiota and Metabolome in Low-Grade vs. High-Grade Dysplastic Colon Polyps: Inference of Their Role in Tumor Initiation and Progression. Cancers (Basel) 2023; 15:3065. [PMID: 37370676 DOI: 10.3390/cancers15123065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
According to the driver-passenger model for colorectal cancer (CRC), the tumor-associated microbiota is a dynamic ecosystem of bacterial species where bacteria with carcinogenic features linked to CRC initiation are defined as "drivers", while opportunistic bacteria colonizing more advanced tumor stages are known as "passengers". We reasoned that also gut microbiota-associated metabolites may be differentially enriched according to tumor stage, and be potential determinants of CRC development. Thus, we characterized the mucosa- and lumen-associated microbiota (MAM and LAM, respectively) and mucosa-associated metabolites in low- vs. high-grade dysplastic colon polyps from 78 patients. We show that MAM, obtained with a new biopsy-preserving approach, and LAM differ in composition and α/β-diversity. By stratifying patients for polyp histology, we found that bacteria proposed as passengers by previous studies colonized high-grade dysplastic adenomas, whereas driver taxa were enriched in low-grade polyps. Furthermore, we report altered "mucosa-associated metabolite" levels in low- vs. high-grade groups. Integrated microbiota-metabolome analysis suggests the involvement of the gut microbiota in the production and consumption of these metabolites. Altogether, our findings support the involvement of bacterial species and associated metabolites in CRC mucosal homeostasis in a tumor-stage-specific manner. These distinct signatures may be used to distinguish low-grade from high-grade dysplastic polyps.
Collapse
Affiliation(s)
| | - Marta La Vecchia
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Marika Sculco
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Soni Joseph
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Elettra Barberis
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Elia Amede
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marta Mellai
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Silvia Brossa
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Giulia Borgonovi
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Pietro Occhipinti
- Department of Gastroenterology, "Maggiore della Carità" Hospital, 28100 Novara, Italy
| | - Renzo Boldorini
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy
| | - Barbara Azzimonti
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Elisa Bona
- Department for Sustainable Development and Ecological Transition, Università del Piemonte Orientale, 13100 Vercelli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Daniela Ferrante
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Anna Aspesi
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Irma Dianzani
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| |
Collapse
|
8
|
Radhakrishnan ST, Gallagher KI, Mullish BH, Serrano-Contreras JI, Alexander JL, Miguens Blanco J, Danckert NP, Valdivia-Garcia M, Hopkins BJ, Ghai A, Ayub A, Li JV, Marchesi JR, Williams HRT. Rectal swabs as a viable alternative to faecal sampling for the analysis of gut microbiota functionality and composition. Sci Rep 2023; 13:493. [PMID: 36627399 DOI: 10.1038/s41598-022-27131-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Faecal or biopsy samples are frequently used to analyse the gut microbiota, but issues remain with the provision and collection of such samples. Rectal swabs are widely-utilised in clinical practice and previous data demonstrate their potential role in microbiota analyses; however, studies to date have been heterogenous, and there are a particular lack of data concerning the utility of swabs for the analysis of the microbiota's functionality and metabolome. We compared paired stool and rectal swab samples from healthy individuals to investigate whether rectal swabs are a reliable proxy for faecal sampling. There were no significant differences in key alpha and beta diversity measures between swab and faecal samples, and inter-subject variability was preserved. Additionally, no significant differences were demonstrated in abundance of major annotated phyla. Inferred gut functionality using Tax4Fun2 showed excellent correlation between the two sampling techniques (Pearson's coefficient r = 0.9217, P < 0.0001). Proton nuclear magnetic resonance (1H NMR) spectroscopy enabled the detection of 20 metabolites, with overall excellent correlation identified between rectal swab and faecal samples for levels all metabolites collectively, although more variable degrees of association between swab and stool for levels of individual metabolites. These data support the utility of rectal swabs in both compositional and functional analyses of the gut microbiota.
Collapse
|
9
|
Chen Y, Si H, Bao B, Li S, Teng D, Yan Y, Hu S, Xu Y, Du X. Integrated analysis of intestinal microbiota and host gene expression in colorectal cancer patients. J Med Microbiol 2022; 71. [PMID: 36136380 DOI: 10.1099/jmm.0.001596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction. Colorectal cancer (CRC) is one of the most common cancers and poses heavy burden on global health. The relationship between mucosal microbiome composition and colorectal gene expression are rarely studied. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between them in colorectal cancer patients.Gap statement. Previous studies have identified the contribution of gut microbiota and DEGs to the pathogenesis of CRC, but the relationship between mucosal microbiome composition and colorectal gene expression are rarely studied.Aim. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between mucosal microbiome composition and colorectal gene expression.Methodology. First, three independent CRC gene expression profiles (GSE184093, GSE156355 and GSE146587) from Gene Expression Omnibus (GEO) were used to identify differentially expressed genes (DEGs). Second, another dataset (GSE163366) was used to analyse gut mucosal microbiome differential abundance. GO (Gene Ontology) function and KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway enrichment analyses of the DEGs were performed. Protein-protein interactions (PPIs) of the DEGs were constructed. The Spearman correlation analysis was computed between host DEGs and gut microbiome abundance data.Results. A total of 1036 upregulated DEGs and 1194 downregulated DEGs between noncancerous tissues and cancerous tissues were identified based on the analysis. One significant module with a score 37.65 was selected out via MCODE including 41 upregulated DEGs, which are were mostly enriched in two pathways, including microtubule binding and tubulin binding. In particular, significant negative correlations are prevalent between Fusobacterium and the 41 DEGs with the correlation ranging between -0.54 and -0.35, and there commonly exist significant positive correlations between Blautia and the 41 DEGs with the correlation ranging between 0.42 and 0.54, indicating that Fusobacterium and Blautia are two of the most important microbes interacting with the gene regulation.Conclusion. Our results demonstrate significant correlation between some gut microbes and DEGs, providing a comprehensive bioinformatics analysis of them for future investigation into the molecular mechanisms and biomarkers.
Collapse
Affiliation(s)
- Yuhui Chen
- Chinese PLA medical school, Beijing, Haidian 100853, PR China.,Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Huiyan Si
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Baoshi Bao
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Songyan Li
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Da Teng
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Yang Yan
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Shidong Hu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Yingxin Xu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| | - Xiaohui Du
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Haidian, Beijing, 100853, PR China
| |
Collapse
|
10
|
Kim N, Gim JA, Lee BJ, Choi BI, Yoon HS, Kim SH, Joo MK, Park JJ, Kim C. Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer. Sci Rep 2022; 12:13447. [PMID: 35927305 DOI: 10.1038/s41598-022-17823-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Various omics-based biomarkers related to the occurrence, progression, and prognosis of colorectal cancer (CRC) have been identified. In this study, we attempted to identify gut microbiome-based biomarkers and detect their association with host gene expression in the initiation and progression of CRC by integrating analysis of the gut mucosal metagenome, RNA sequencing, and sociomedical factors. We performed metagenome and RNA sequencing on colonic mucosa samples from 13 patients with advanced CRC (ACRC), 10 patients with high-risk adenoma (HRA), and 7 normal control (NC) individuals. All participants completed a questionnaire on sociomedical factors. The interaction and correlation between changes in the microbiome and gene expression were assessed using bioinformatic analysis. When comparing HRA and NC samples, which can be considered to represent the process of tumor initiation, 28 genes and five microbiome species were analyzed with correlation plots. When comparing ACRC and HRA samples, which can be considered to represent the progression of CRC, seven bacterial species and 21 genes were analyzed. When comparing ACRC and NC samples, 16 genes and five bacterial species were analyzed, and four correlation plots were generated. A network visualizing the relationship between bacterial and host gene expression in the initiation and progression of CRC indicated that Clostridium spiroforme and Tyzzerella nexilis were hub bacteria in the development and progression of CRC. Our study revealed the interactions of and correlation between the colonic mucosal microbiome and host gene expression to identify potential roles of the microbiome in the initiation and progression of CRC. Our results provide gut microbiome-based biomarkers that may be potential diagnostic markers and therapeutic targets in patients with CRC.
Collapse
|
11
|
Qin X, Bi L, Yang W, He Y, Gu Y, Yang Y, Gong Y, Wang Y, Yan X, Xu L, Xiao H, Jiao L. Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer. Front Microbiol 2022; 13:918823. [PMID: 35774470 PMCID: PMC9237568 DOI: 10.3389/fmicb.2022.918823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022] Open
Abstract
Lung cancer is a malignancy with high incidence and mortality worldwide. Previous studies have shown that the gut microbiome plays an important role in the development and progression of metabolic cancers. However, data on the characteristics of the gut microbiome with different histopathology types of lung cancer remain scant. We collected stool samples from 28 healthy people (HP) and 61 lung cancer patients. The lung cancer patients were classified into three types according to their histopathology: Atypical Adenomatous Hyperplasia/Adenocarcinoma in situ (AAH/AIS), Minimally Invasive Adenocarcinoma (MIA), and Invasive Adenocarcinoma (IA). In addition, we employed 16S rRNA gene amplicon sequencing to analyze the characteristics of the gut microbiome in these patients. Our analysis revealed that the categorized cancer patients had unique intestinal flora characteristics, and had lower density and flora diversity compared to healthy people. Besides, the structure of the flora families and genera was more complex, and each group presented specific pathogenic microbiota. The patients in the AAH/AIS group and HP group had relatively similar flora structure compared with the IA and MIA groups. In addition, we identified several flora markers that showed significant changes with the development of lung cancer. Lung cancer gut microbiota showed a decrease in short-chain fatty acids (SCFAs) producing and anti-inflammatory bacteria compared to healthy people, while some pathogenic bacteria such as proinflammatory or tumor-promoting bacteria were more abundant in lung cancer patients. On the other hand, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Group (COG) annotation demonstrated suppression of some dominant metabolism-related pathways in lung cancer. These findings provide new biomarkers for the diagnosis and prognostic assessment of lung cancer and lay the basis for novel targeted therapeutic strategies for the prevention and treatment of lung cancer.
Collapse
Affiliation(s)
- Xiong Qin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Ling Bi
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenxiao Yang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiyun He
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifeng Gu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yabin Gong
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yichao Wang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxia Yan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Ling Xu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Haibo Xiao
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Haibo Xiao,
| | - Lijing Jiao
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Institute of Clinical Immunology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Lijing Jiao,
| |
Collapse
|
12
|
Xu Y, Nash K, Acharjee A, Gkoutos GV. CACONET: a novel classification framework for microbial correlation networks. Bioinformatics 2022; 38:1639-1647. [PMID: 34983063 PMCID: PMC8896646 DOI: 10.1093/bioinformatics/btab879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/15/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease. RESULTS We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility. AVAILABILITY AND IMPLEMENTATION CACONET is available at https://github.com/yuanwxu/corr-net-classify. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yuanwei Xu
- To whom correspondence should be addressed.
| | - Katrina Nash
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham B15 2TT, UK,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK,MRC Health Data Research UK (HDR), Midlands Site B15 2TT, UK
| | - Georgios V Gkoutos
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham B15 2TT, UK,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK,MRC Health Data Research UK (HDR), Midlands Site B15 2TT, UK
| |
Collapse
|
13
|
Dessì A, Tognazzi C, Bosco A, Pintus R, Fanos V. Metabolomic profiles and microbiota of GDM offspring: The key for future perspective? Front Pediatr 2022; 10:941800. [PMID: 36275053 PMCID: PMC9579340 DOI: 10.3389/fped.2022.941800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Gestational diabetes mellitus (GDM), or any degree of glucose intolerance recognized for the first time during pregnancy, is one of the diseases that most frequently aggravates the course of gestation. Missed or late diagnosis and inadequate treatment are associated with high maternal and fetal morbidity, with possible short- and long-term repercussions. Estimates on the prevalence of GDM are alarming and increasing by about 30% in the last 10-20 years. In addition, there is the negative influence of the SARS-CoV-2 emergency on the glycemic control of pregnant women, making the matter increasingly topical. To date, knowledge on the metabolic maturation of newborns is still incomplete. However, in light of the considerable progress of the theory of "developmental origins of health and disease," the relevant role of the intrauterine environment cannot be overlooked. In fact, due to the high plasticity of the early stages of development, some detrimental metabolic alterations during fetal growth, including maternal hyperglycemia, are associated with a higher incidence of chronic diseases in adult life. In this context, metabolomic analysis which allows to obtain a detailed phenotypic portrait through the dynamic detection of all metabolites in cells, tissues and different biological fluids could be very useful for the early diagnosis and prevention of complications. Indeed, if the diagnostic timing is optimized through the identification of specific metabolites, the detailed understanding of the altered metabolic pathway could also allow better management and more careful monitoring, also from a nutritional profile, of the more fragile children. In this context, a further contribution derives from the analysis of the intestinal microbiota, the main responsible for the fecal metabolome, given its alteration in pregnancies complicated by GDM and the possibility of transmission to offspring. The purpose of this review is to analyze the available data regarding the alterations in the metabolomic profile and microbiota of the offspring of mothers with GDM in order to highlight future prospects for reducing GDM-related complications in children of mothers affected by this disorder.
Collapse
Affiliation(s)
- Angelica Dessì
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Azienda Ospedaliera Universitaria (AOU) Cagliari, University of Cagliari, Cagliari, Italy
| | - Chiara Tognazzi
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Azienda Ospedaliera Universitaria (AOU) Cagliari, University of Cagliari, Cagliari, Italy
| | - Alice Bosco
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Azienda Ospedaliera Universitaria (AOU) Cagliari, University of Cagliari, Cagliari, Italy
| | - Roberta Pintus
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Azienda Ospedaliera Universitaria (AOU) Cagliari, University of Cagliari, Cagliari, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Azienda Ospedaliera Universitaria (AOU) Cagliari, University of Cagliari, Cagliari, Italy
| |
Collapse
|